PF3D7_1406900 (RlmN)

Genome location: Pf3D7_14_v3:250,334..252,921(+)

Genome classification: Core

Function and Localization

Product Description: radical SAM protein, putative

SignalP Peptide: N/A

# Transmembrane Domains: 0

EC Numbers: None

Curated GO (PlasmoDB):

Type	GO Term	Name
Component	GO:0005741	mitochondrial outer membrane
Process	GO:0070475	rRNA base methylation
Process	GO:0030488	tRNA methylation

Expression by stage (LR - Le Roch et al., and MCA - Malaria Cell Atlas):

Stage	LR class	MCA mean	MCA prop. zeros
Sporozoite	expressed	N/A	N/A
Ring	possibly expressed	0.02	0.99
Trophozoite	expressed	0.09	0.94
Schizont	expressed	0.07	0.95
Gametocyte	expressed	0.13	0.92

More info:

Resistome Mutations

Old (Pf3D7v3) Gene ID: PF3D7_1406900

Resistome Missense Mutations: None

Resistome Compounds with Missense Mutations: None

Resistome # Samples with Disruptive Mutations: 0 (0 missense, 0 "interesting" missense)

Essentiality (ABS)

Zhang Phenotype: Non - Mutable in CDS

MIS: 0.119 | MFS: -2.957 | #Insertions: 0

PlasmoGEM Phenotype: Essential (Pb ortholog: PBANKA_1035300)

Relative Growth Rate: 0.13 ± 0.16
Confidence: 5.01

RMgmDB ABS Phenotype: N/A

More info: PhenoPlasm Link

Binding Evidence

AlphaFill Uniprot ID: Q8IM25

"Best" AlphaFill ligand hit: SAM (s-adenosylmethionine, Local RMSD=0.48) with 3RFA (Global RMSD=3.02)

No associated EC numbers

No evidence of orthology to BindingDB entries

Orthology Information

Ortholog Group (OrthoMCL): OG6_102893

No human ortholog(s)

Genetic Variation

MalariaGEN Pf7 (worldwide samples) # unique SNV/indels:

Homozygous genotype calls only

variant type	common	rare	doubleton	singleton
synonymous	1	24	10	29
disruptive	3	31	13	44
missense	3	31	13	39

Any inclusion in genotype call

variant type	common	rare	doubleton	singleton
synonymous	6	39	23	24
disruptive	7	58	33	66
missense	6	56	29	46

PlasmoDB Total SNPs: 147

Non-coding: 137 | Synonymous: 5 | Nonsynonymous: 5 | Stop Codon: 0

Protein Information

Protein Length: 362 | Molecular Weight (kDa): 42.327

UniProt ID(s): Q8IM25

PDB ID(s): None

Isoelectric Point: 9.71

Protein Domain Annotations:

Source	Family ID	Description
InterPro	IPR004383	Ribosomal RNA large subunit methyltransferase RlmN/Cfr
InterPro	IPR007197	Radical SAM
InterPro	IPR040072	Methyltransferase (Class A)
PFam	PF04055	Radical SAM
Superfamily	SSF102114	N/A

Associated Publications

PMID	Title	Authors	DOI/Link
12368864	Genome sequence of the human malaria parasite Plasmodium falciparum.	Gardner MJ, Hall N, ..., Barrell B	10.1038/nature01097
29293520	Elp3 and RlmN: A tale of two mitochondrial tail-anchored radical SAM enzymes inToxoplasma gondii.	Padgett LR, Lentini JM, ..., Sullivan WJ Jr	10.1371/journal.pone.0189688
29787246	Investigation of Solvent Hydron Exchange in the Reaction Catalyzed by theAntibiotic Resistance Protein Cfr	Bauerle MR, Grove TL, Booker SJ	10.1021/acs.biochem.8b00347
28643349	A QM/MM study of the catalytic mechanism of SAM methyltransferase RlmN from Escherichia coli	Zhao C, Dong L, Liu Y	10.1002/prot.25337
35481783	RNA Post-Transcriptional Modifications in Two Large Subunit Intermediates Populated in E. coli Cells Expressing Helicase Inactive R331A DbpA	Koculi E, Cho SS	10.1021/acs.biochem.2c00096